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Dong X, Zhang H, Zhu X, Wang K, Xue H, Ye Z, Zheng C, Bu W. Mitochondrial introgression and mito-nuclear discordance obscured the closely related species boundaries in Cletus Stål from China (Heteroptera: Coreidae). Mol Phylogenet Evol 2023; 184:107802. [PMID: 37221926 DOI: 10.1016/j.ympev.2023.107802] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2022] [Revised: 04/07/2023] [Accepted: 04/18/2023] [Indexed: 05/25/2023]
Abstract
Accurate taxonomy and delimitation are of great importance for pest control strategies and management programs. Here, we focus on Cletus (Insecta: Hemiptera: Coreidae), which includes many crop pests. The species boundaries still conflict and only cytochrome c oxidase subunit I (COI) barcoding has been previously used for molecular studies. We generated new mitochondrial genome and nuclear genome-wide SNPs to explore the species boundaries of 46 Cletus samples from China using multiple species delimitation approaches. All results recovered a monophyly with high support, except for two closely related species in clade I - C. punctiger and C. graminis. Mitochondrial data demonstrated admixture in clade I, while genome-wide SNPs unambiguously identified two separate species, which were confirmed by morphological classification. Inconsistent nuclear and mitochondrial data indicated mito-nuclear discordance. Mitochondrial introgression is the most likely explanation, and more extensive sampling and more comprehensive data are needed to ascertain a pattern. Accurate species delimitation will shed light on species status; thus, an accurate taxonomy is of particular concern, as there is a pressing need to implement precise control of agricultural pests and to perform further research on diversification.
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Affiliation(s)
- Xue Dong
- Institute of Entomology, College of Life Sciences, Nankai University, Tianjin 300071, China
| | - Haiguang Zhang
- College of Life Science, Linyi University, Linyi 276000, China
| | - Xiuxiu Zhu
- Institute of Entomology, College of Life Sciences, Nankai University, Tianjin 300071, China
| | - Kaibin Wang
- Institute of Entomology, College of Life Sciences, Nankai University, Tianjin 300071, China
| | - Huaijun Xue
- Institute of Entomology, College of Life Sciences, Nankai University, Tianjin 300071, China
| | - Zhen Ye
- Institute of Entomology, College of Life Sciences, Nankai University, Tianjin 300071, China.
| | - Chenguang Zheng
- Institute of Entomology, College of Life Sciences, Nankai University, Tianjin 300071, China.
| | - Wenjun Bu
- Institute of Entomology, College of Life Sciences, Nankai University, Tianjin 300071, China.
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2
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Zhou LY, Zhan ZH, Zhu XL, Wan X. Multilocus phylogeny and species delimitation suggest synonymies of two Lucanus Scopoli, 1763 (Coleoptera, Lucanidae) species names. Zookeys 2022; 1135:139-155. [PMID: 36761796 PMCID: PMC9836572 DOI: 10.3897/zookeys.1135.89257] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2022] [Accepted: 11/23/2022] [Indexed: 12/15/2022] Open
Abstract
Phylogenetic relationsships of four nominal Lucanus Scopoli, 1763 species, L.swinhoei Parry, 1874, L.continentalis Zilioli, 1998, L.liuyei Huang & Chen, 2010, and L.wuyishanensis Schenk, 1999, are assessed based on mitochondrial (16S rDNA, COI) and nuclear (28S rDNA, Wingless) genes. The genetic distance is 0.0072 between L.swinhoei and L.continentalis, and 0.0094 between L.wuyishanensis and L.liuyei. Three species-delimitation approaches (ABGD, PTP, and GMYC) consistently showed L.swinhoei + L.continentalis and L.wuyishanensis + L.liuyei as two MOTUs. A new synonymy, L.liuyei = L.wuyishanensis, is proposed. Synonymy of L.swinhoei over L.continentalis is confirmed.
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Affiliation(s)
- Li Yang Zhou
- Department of Ecology, School of Resources and Engineering, Anhui University, 111 Jiulong Rd., Hefei 230601, China
| | - Zhi Hong Zhan
- Anhui Province Key Laboratory of Wetland Ecosystem Protection and Restoration, Anhui University, 111 Jiulong Rd., Hefei, 230601, China
| | - Xue Li Zhu
- Department of Ecology, School of Resources and Engineering, Anhui University, 111 Jiulong Rd., Hefei 230601, China
| | - Xia Wan
- Department of Ecology, School of Resources and Engineering, Anhui University, 111 Jiulong Rd., Hefei 230601, China
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3
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Dong X, Yi W, Zheng C, Zhu X, Wang S, Xue H, Ye Z, Bu W. Species delimitation of rice seed bugs complex: Insights from mitochondrial genomes and ddRAD‐seq data. ZOOL SCR 2021. [DOI: 10.1111/zsc.12523] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Xue Dong
- Institute of Entomology College of Life Sciences Nankai University Tianjin China
| | - Wenbo Yi
- Department of Biology Xinzhou Teachers University Xinzhou China
| | - Chenguang Zheng
- Institute of Entomology College of Life Sciences Nankai University Tianjin China
| | - Xiuxiu Zhu
- Institute of Entomology College of Life Sciences Nankai University Tianjin China
| | - Shujing Wang
- Institute of Entomology College of Life Sciences Nankai University Tianjin China
| | - Huaijun Xue
- Institute of Entomology College of Life Sciences Nankai University Tianjin China
| | - Zhen Ye
- Institute of Entomology College of Life Sciences Nankai University Tianjin China
| | - Wenjun Bu
- Institute of Entomology College of Life Sciences Nankai University Tianjin China
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Lin X, Zhao Y, Yan L, Liu W, Bu W, Wang X, Zheng C. Mitogenomes provide new insights into the evolutionary history of Prodiamesinae (Diptera: Chironomidae). ZOOL SCR 2021. [DOI: 10.1111/zsc.12516] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Affiliation(s)
- Xiao‐Long Lin
- College of Life Sciences Nankai University Tianjin China
| | - Yan‐Min Zhao
- State Key Laboratory of Environmental Criteria and Risk Assessment Chinese Research Academy of Environmental Sciences Beijing China
| | - Li‐Ping Yan
- School of Ecology and Nature Conservation Beijing Forestry University Beijing China
| | - Wen‐Bin Liu
- Tianjin Key Laboratory of Conservation and Utilization of Animal Diversity Tianjin Normal University Tianjin China
| | - Wen‐Jun Bu
- College of Life Sciences Nankai University Tianjin China
| | - Xin‐Hua Wang
- College of Life Sciences Nankai University Tianjin China
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5
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Crespo LC, Silva I, Enguídanos A, Cardoso P, Arnedo MA. The Atlantic connection: coastal habitat favoured long distance dispersal and colonization of Azores and Madeira by Dysdera spiders (Araneae: Dysderidae). SYST BIODIVERS 2021. [DOI: 10.1080/14772000.2021.1946618] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Affiliation(s)
- Luís C. Crespo
- Department of Evolutionary Biology, Ecology and Environmental Sciences (Arthropods), Biodiversity Research Institute (IRBio), University of Barcelona, Avd. Diagonal, 643, Barcelona, 08028, Spain
- Laboratory for Integrative Biodiversity Research (LIBRe), Finnish Museum of Natural History, Helsinki, 00014, Finland
| | - Isamberto Silva
- Instituto das Florestas e Conservação da Natureza, Funchal, 9054-505, Portugal
| | - Alba Enguídanos
- Department of Evolutionary Biology, Ecology and Environmental Sciences (Arthropods), Biodiversity Research Institute (IRBio), University of Barcelona, Avd. Diagonal, 643, Barcelona, 08028, Spain
| | - Pedro Cardoso
- Laboratory for Integrative Biodiversity Research (LIBRe), Finnish Museum of Natural History, P.O. Box 17, Helsinki, 00014, Finland
- University of Helsinki, Helsinki, 00014, Finland
| | - Miquel A. Arnedo
- Department of Evolutionary Biology, Ecology and Environmental Sciences (Arthropods), Biodiversity Research Institute (IRBio), University of Barcelona, Avd. Diagonal, 643, Barcelona, 08028, Spain
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Abstract
Bermuda is an Eocene age volcanic island in the western North Atlantic, entirely capped by Pleistocene eolian limestone. The oldest and most highly karstified limestone is a 2 km2 outcrop of the Walsingham Formation containing most of the island’s 150+ caves. Extensive networks of submerged cave passageways, flooded by saltwater, extend under the island. In the early 1980s, cave divers initially discovered an exceptionally rich and diverse anchialine community inhabiting deeper sections of the caves. The fauna inhabiting caves in the Walsingham Tract consists of 78 described species of cave-dwelling invertebrates, including 63 stygobionts and 15 stygophiles. Thus, it represents one of the world’s top hotspots of subterranean biodiversity. Of the anchialine fauna, 65 of the 78 species are endemic to Bermuda, while 66 of the 78 are crustaceans. The majority of the cave species are limited in their distribution to just one or only a few adjacent caves. Due to Bermuda’s high population density, water pollution, construction, limestone quarries, and trash dumping produce severe pressures on cave fauna and groundwater health. Consequently, the IUCN Red List includes 25 of Bermuda’s stygobiont species as critically endangered.
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Siriwut W, Jeratthitikul E, Panha S, Chanabun R, Ngor PB, Sutcharit C. Evidence of cryptic diversity in freshwater Macrobrachium prawns from Indochinese riverine systems revealed by DNA barcode, species delimitation and phylogenetic approaches. PLoS One 2021; 16:e0252546. [PMID: 34077477 PMCID: PMC8171930 DOI: 10.1371/journal.pone.0252546] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2021] [Accepted: 05/18/2021] [Indexed: 12/04/2022] Open
Abstract
The diversity of Indochinese prawns in genus Macrobrachium is enormous due to the habitat diversification and broad tributary networks of two river basins: the Chao Phraya and the Mekong. Despite long-standing interest in SE-Asian decapod diversity, the subregional Macrobrachium fauna is still not yet comprehensively clarified in terms of taxonomic identification or genetic diversification. In this study, integrative taxonomic approaches including morphological examination, DNA barcoding, and molecular species delimitation were used to emphasize the broad scale systematics of Macrobrachium prawns in Indochina. Twenty-seven nominal species were successfully re-verified by traditional and molecular taxonomy. Barcode gap analysis supported broad overlapping of species boundaries. Taxonomic ambiguity of several deposited samples in the public database is related to inter- and intraspecific genetic divergence as indicated by BOLD discordance. Diagnostic nucleotide positions were found in six Macrobrachium species. Eighteen additional putative lineages are herein assigned using the consensus of species delimitation methods. Genetic divergence indicates the possible existence of cryptic species in four morphologically complex and wide-ranging species: M. lanchesteri, M. niphanae, M. sintangense, and some members of the M. pilimanus group. The geographical distribution of some species supports the connections and barriers attributed to paleo-historical events of SE-Asian rivers and land masses. Results of this study show explicitly the importance of freshwater ecosystems in Indochinese subregions, especially for the Mekong River Basin due to its high genetic diversity and species composition found throughout its tributaries.
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Affiliation(s)
- Warut Siriwut
- Animal Systematics and Molecular Ecology Laboratory, Department of Biology, Faculty of Science, Mahidol University, Bangkok, Thailand
| | - Ekgachai Jeratthitikul
- Animal Systematics and Molecular Ecology Laboratory, Department of Biology, Faculty of Science, Mahidol University, Bangkok, Thailand
| | - Somsak Panha
- Animal Systematics Research Unit, Department of Biology, Faculty of Science, Chulalongkorn University, Bangkok, Thailand
- Academy of Science, The Royal Society of Thailand, Dusit, Bangkok, Thailand
| | - Ratmanee Chanabun
- Program in Animal Science, Faculty of Agricultural Technology, Sakon Nakhon Rajabhat University, Sakon Nakhon, Thailand
| | - Peng Bun Ngor
- Inland Fisheries Research and Development Institute (IFReDI), Fisheries Administration, Phnom Penh, Cambodia
- Wonders of the Mekong Project, Phnom Penh, Cambodia
| | - Chirasak Sutcharit
- Animal Systematics Research Unit, Department of Biology, Faculty of Science, Chulalongkorn University, Bangkok, Thailand
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8
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Zheng CG, Zhu XX, Yan LP, Yao Y, Bu WJ, Wang XH, Lin XL. First complete mitogenomes of Diamesinae, Orthocladiinae, Prodiamesinae, Tanypodinae (Diptera: Chironomidae) and their implication in phylogenetics. PeerJ 2021; 9:e11294. [PMID: 33996279 PMCID: PMC8106913 DOI: 10.7717/peerj.11294] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2020] [Accepted: 03/27/2021] [Indexed: 11/20/2022] Open
Abstract
BACKGROUND The mitochondrial genome (mitogenome) has been extensively used for phylogenetic and evolutionary analysis in Diptera, but the study of mitogenome is still scarce in the family Chironomidae. METHODS Here, the first complete mitochondrial genomes of four Chironomid species representing Diamesinae, Orthocladiinae, Prodiamesinae and Tanypodinae are presented. Coupled with published mitogenomes of two, a comparative mitochondrial genomic analysis between six subfamilies of Chironomidae was carried out. RESULTS Mitogenomes of Chironomidae are conserved in structure, each contains 37 typical genes and a control region, and all genes arrange the same gene order as the ancestral insect mitogenome. Nucleotide composition is highly biased, the control region displayed the highest A + T content. All protein coding genes are under purifying selection, and the ATP8 evolves at the fastest rate. In addition, the phylogenetic analysis covering six subfamilies within Chironomidae was conducted. The monophyly of Chironomidae is strongly supported. However, the topology of six subfamilies based on mitogenomes in this study is inconsistent with previous morphological and molecular studies. This may be due to the high mutation rate of the mitochondrial genetic markers within Chironomidae. Our results indicate that mitogenomes showed poor signals in phylogenetic reconstructions at the subfamily level of Chironomidae.
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Affiliation(s)
| | - Xiu-Xiu Zhu
- College of Life Sciences, Nankai University, Tianjin, China
| | - Li-Ping Yan
- School of Ecology and Nature Conservation, Beijing Forestry University, Beijing, China
| | - Yuan Yao
- College of Life Sciences, Tianjin Normal University, Tianjin, China
| | - Wen-Jun Bu
- College of Life Sciences, Nankai University, Tianjin, China
| | - Xin-Hua Wang
- College of Life Sciences, Nankai University, Tianjin, China
| | - Xiao-Long Lin
- College of Life Sciences, Nankai University, Tianjin, China
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9
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Boulaassafer K, Ghamizi M, Machordom A, Albrecht C, Delicado D. Hidden species diversity of Corrosella Boeters, 1970 (Caenogastropoda: Truncatelloidea) in the Moroccan Atlas reveals the ancient biogeographic link between North Africa and Iberia. ORG DIVERS EVOL 2021. [DOI: 10.1007/s13127-021-00490-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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10
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Yuan JJ, Chen D, Wan X. A multilocus assessment reveals two new synonymies for East Asian Cyclommatus stag beetles (Coleoptera, Lucanidae). Zookeys 2021; 1021:65-79. [PMID: 33727883 PMCID: PMC7943532 DOI: 10.3897/zookeys.1021.58832] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2020] [Accepted: 01/31/2021] [Indexed: 11/12/2022] Open
Abstract
Cyclommatus scutellaris Möllenkamp, 1912, Cyclommatus elsae Kriesche, 1921 and Cyclommatus tamdaoensis Fujita, 2010 are East Asian stag beetle species with long-debated taxonomic relationships due to high intraspecific morphological variability. In this study, we applied multilocus phylogenetic analyses to reassess their relationships. Two mitochondrial genes (16S rDNA, COI) and two nuclear genes (28S rDNA, Wingless) were used to reconstruct the phylogeny through the Bayesian inference (BI) and Maximum Likelihood (ML) methods. Both topologies supported two clades: the clade C. scutellaris was sister to the clade (C. elsae + C. tamdaoensis) with the subclade C. tamdaoensis embedded in the subclade C. elsae. The Kimura 2-parameter (K2P) genetic distance analysis yielded a low mean value (≤0.035) among the three taxa, which was well below the minimum mean value between other Cyclommatus species (≥0.122). We also compared the accuracy and efficiency of two approaches, GMYC and ABGD, in delimitating the three lineages. The result shows that ABGD is a better approach than GMYC. Our molecular data recognizes the three species as different populations of a single species, ranging from Taiwan Island to the continent. Therefore, we propose two new junior synonyms for C. scutellaris: C. tamdaoensis, syn. nov. and C. elsae syn. nov.
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Affiliation(s)
- Jiao Jiao Yuan
- Department of Ecology, School of Resources and Engineering, Anhui University, 111 Jiulong Rd., Hefei 230601, China Anhui University Hefei China.,Anhui Province Key Laboratory of Wetland Ecosystem Protection and Restoration, Hefei 230601, China Anhui Province Key Laboratory of Wetland Ecosystem Protection and Restoration Hefei China
| | - Dan Chen
- Department of Ecology, School of Resources and Engineering, Anhui University, 111 Jiulong Rd., Hefei 230601, China Anhui University Hefei China.,Anhui Province Key Laboratory of Wetland Ecosystem Protection and Restoration, Hefei 230601, China Anhui Province Key Laboratory of Wetland Ecosystem Protection and Restoration Hefei China
| | - Xia Wan
- Department of Ecology, School of Resources and Engineering, Anhui University, 111 Jiulong Rd., Hefei 230601, China Anhui University Hefei China.,Anhui Province Key Laboratory of Wetland Ecosystem Protection and Restoration, Hefei 230601, China Anhui Province Key Laboratory of Wetland Ecosystem Protection and Restoration Hefei China
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Plazzi F, Puccio G, Passamonti M. HERMES: An improved method to test mitochondrial genome molecular synapomorphies among clades. Mitochondrion 2021; 58:285-295. [PMID: 33639269 DOI: 10.1016/j.mito.2021.02.009] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2020] [Revised: 01/10/2021] [Accepted: 02/12/2021] [Indexed: 02/06/2023]
Abstract
Mitochondrial chromosomes have diversified among eukaryotes and many different architectures and features are now acknowledged for this genome. Here we present the improved HERMES index, which can measure and quantify the amount of molecular change experienced by mitochondrial genomes. We test the improved approach with ten molecular phylogenetic studies based on complete mitochondrial genomes, representing six bilaterian Phyla. In most cases, HERMES analysis spotted out clades or single species with peculiar molecular synapomorphies, allowing to identify phylogenetic and ecological patterns. The software presented herein handles linear, circular, and multi-chromosome genomes, thus widening the HERMES scope to the complete eukaryotic domain.
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Affiliation(s)
- Federico Plazzi
- Department of Biological, Geological and Environmental Sciences, University of Bologna, via Selmi, 3, 40126 Bologna, Italy.
| | - Guglielmo Puccio
- Department of Biological, Geological and Environmental Sciences, University of Bologna, via Selmi, 3, 40126 Bologna, Italy.
| | - Marco Passamonti
- Department of Biological, Geological and Environmental Sciences, University of Bologna, via Selmi, 3, 40126 Bologna, Italy.
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12
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Zapelloni F, Jurado-Rivera JA, Jaume D, Juan C, Pons J. Comparative Mitogenomics in Hyalella (Amphipoda: Crustacea). Genes (Basel) 2021; 12:genes12020292. [PMID: 33669879 PMCID: PMC7923271 DOI: 10.3390/genes12020292] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2021] [Revised: 02/16/2021] [Accepted: 02/17/2021] [Indexed: 02/02/2023] Open
Abstract
We present the sequencing and comparative analysis of 17 mitochondrial genomes of Nearctic and Neotropical amphipods of the genus Hyalella, most from the Andean Altiplano. The mitogenomes obtained comprised the usual 37 gene-set of the metazoan mitochondrial genome showing a gene rearrangement (a reverse transposition and a reversal) between the North and South American Hyalella mitogenomes. Hyalella mitochondrial genomes show the typical AT-richness and strong nucleotide bias among codon sites and strands of pancrustaceans. Protein-coding sequences are biased towards AT-rich codons, with a preference for leucine and serine amino acids. Numerous base changes (539) were found in tRNA stems, with 103 classified as fully compensatory, 253 hemi-compensatory and the remaining base mismatches and indels. Most compensatory Watson–Crick switches were AU -> GC linked in the same haplotype, whereas most hemi-compensatory changes resulted in wobble GU and a few AC pairs. These results suggest a pairing fitness increase in tRNAs after crossing low fitness valleys. Branch-site level models detected positive selection for several amino acid positions in up to eight mitochondrial genes, with atp6 and nad5 as the genes displaying more sites under selection.
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Affiliation(s)
- Francesco Zapelloni
- Department of Biology, University of the Balearic Islands, Ctra. Valldemossa km 7,5, 07122 Palma, Spain; (F.Z.); (J.A.J.-R.); (C.J.)
| | - José A. Jurado-Rivera
- Department of Biology, University of the Balearic Islands, Ctra. Valldemossa km 7,5, 07122 Palma, Spain; (F.Z.); (J.A.J.-R.); (C.J.)
| | - Damià Jaume
- IMEDEA (CSIC-UIB), Mediterranean Institute for Advanced Studies, C/Miquel Marquès 21, 07190 Esporles, Spain;
| | - Carlos Juan
- Department of Biology, University of the Balearic Islands, Ctra. Valldemossa km 7,5, 07122 Palma, Spain; (F.Z.); (J.A.J.-R.); (C.J.)
- IMEDEA (CSIC-UIB), Mediterranean Institute for Advanced Studies, C/Miquel Marquès 21, 07190 Esporles, Spain;
| | - Joan Pons
- IMEDEA (CSIC-UIB), Mediterranean Institute for Advanced Studies, C/Miquel Marquès 21, 07190 Esporles, Spain;
- Correspondence: ; Tel.: +34-971-173-332
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Núñez J, Glasby CJ, Naranjo M. Groundwater annelids from Gran Canaria and Fuerteventura (Canary Islands), with the description of two new species of Namanereis (Namanereidinae, Nereididae, Polychaeta). SUBTERRANEAN BIOLOGY 2020. [DOI: 10.3897/subtbiol.36.55090] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
The Canary Islands are the richest volcanic region in the world in subterranean adapted fauna, followed by the Hawaiian Islands and the Undara Cave in Australia. Most of the subterranean adapted aquatic fauna from the Canary Islands is restricted to the anchialine environments in La Corona lava tube in Lanzarote, while the oligohaline stygobiont fauna, usually found in groundwater or interstitial freshwaters, is scarcer and represented by a few species of amphipods, copepods, and a single polychaete annelid recorded from Fuerteventura and doubtfully identified as Namanereis hummelincki (non Augener, 1933) (Hartmann-Schröder, 1988). Two new species of polychaete annelids belonging to the subfamily Namanereidinae are described from Gran Canaria and Fuerteventura. Both species live in groundwater, are depigmented and eyeless, and have bifid jaws. Although they are seemingly more related to each other than to other members of the bifid-jaw group, Namanereis canariarumsp. nov. can be diagnosed by its relatively longer tentacular cirri and parapodial dorsal cirri, as well as the presence of pseudospiniger chaetae. In contrast, Namanereis llanetensissp. nov. has shorter cirri and usually lacks pseudospiniger chaetae. Namanereis canariarumsp. nov. and Namanereis llanetensissp. nov. increase to 20 the total number of currently described species within this enigmatic genus. More than half of those species are adapted to live in groundwaters.
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14
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Narakusumo RP, Riedel A, Pons J. Mitochondrial genomes of twelve species of hyperdiverse Trigonopterus weevils. PeerJ 2020; 8:e10017. [PMID: 33083123 PMCID: PMC7566755 DOI: 10.7717/peerj.10017] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2020] [Accepted: 09/01/2020] [Indexed: 11/20/2022] Open
Abstract
Mitochondrial genomes of twelve species of Trigonopterus weevils are presented, ten of them complete. We describe their gene order and molecular features and test their potential for reconstructing the phylogeny of this hyperdiverse genus comprising > 1,000 species. The complete mitochondrial genomes examined herein ranged from 16,501 bp to 21,007 bp in length, with an average AT content of 64.2% to 69.7%. Composition frequencies and skews were generally lower across species for atp6, cox1-3, and cob genes, while atp8 and genes coded on the minus strand showed much higher divergence at both nucleotide and amino acid levels. Most variation within genes was found at the codon level with high variation at third codon sites across species, and with lesser degree at the coding strand level. Two large non-coding regions were found, CR1 (between rrnS and trnI genes) and CR2 (between trnI and trnQ), but both with large variability in length; this peculiar structure of the non-coding region may be a derived character of Curculionoidea. The nad1 and cob genes exhibited an unusually high interspecific length variation of up to 24 bp near the 3' end. This pattern was probably caused by a single evolutionary event since both genes are only separated by trnS2 and length variation is extremely rare in mitochondrial protein coding genes. We inferred phylogenetic trees using protein coding gene sequences implementing both maximum likelihood and Bayesian approaches, each for both nucleotide and amino acid sequences. While some clades could be retrieved from all reconstructions with high confidence, there were also a number of differences and relatively low support for some basal nodes. The best partition scheme of the 13 protein coding sequences obtained by IQTREE suggested that phylogenetic signal is more accurate by splitting sequence variation at the codon site level as well as coding strand, rather than at the gene level. This result corroborated the different patterns found in Trigonopterus regarding to A+T frequencies and AT and GC skews that also greatly diverge at the codon site and coding strand levels.
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Affiliation(s)
- Raden Pramesa Narakusumo
- State Museum of Natural History Karlsruhe, Karlsruhe, Germany.,Museum Zoologicum Bogoriense, Research Center for Biology, Indonesian Institute of Sciences (LIPI), Cibinong, Indonesia
| | | | - Joan Pons
- Diversidad Animal y Microbiana, Instituto Mediterráneo de Estudios Avanzados IMEDEA (CSIC-UIB), Esporles, Balearic Islands, Spain
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15
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González-Castellano I, Pons J, González-Ortegón E, Martínez-Lage A. Mitogenome phylogenetics in the genus Palaemon (Crustacea: Decapoda) sheds light on species crypticism in the rockpool shrimp P. elegans. PLoS One 2020; 15:e0237037. [PMID: 32810189 PMCID: PMC7444591 DOI: 10.1371/journal.pone.0237037] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2020] [Accepted: 07/17/2020] [Indexed: 12/24/2022] Open
Abstract
The genus Palaemon comprises worldwide marine and freshwater shrimps and prawns, and some of them are ecologically or commercially important species. Palaemon is not currently a monophyletic group, so phylogenetics and systematics are constantly changing. Species crypticism has been pointed out in several Palaemon species, being the clearest evidence in the European rockpool shrimp P. elegans. Here we sequenced and described seven European Palaemon mitochondrial genomes. The mitochondrial protein-coding genes were used, along with those of three other Palaemon species, to perform mitogenome phylogenetic analyses to clarify the evolutionary relationships within the genus, and particularly to shed light on the cryptic species found within P. elegans. The Messinian Salinity Crisis (5.3-5.9 Ma, late Miocene) was proposed to be the origin of this cryptic species and it was used as aged constraint for calibration analysis. We provide the largest and the first time-calibrated mitogenome phylogeny of the genus Palaemon and mitogenome substitution rate was estimated (1.59% per million years) in Decapoda for the first time. Our results highlighted the need for future systematics changes in Palaemon and crypticism in P. elegans was confirmed. Mitochondrial genome and cox1 (1.41%) substitution rate estimates matched those published elsewhere, arguing that the Messinian Salinity Crisis was a plausible event driving the split between P. elegans and its cryptic species. Molecular dating suggested that Pleistocene glaciations were likely involved in the differentiation between the Atlantic and Mediterranean populations of P. elegans. On the contrary, the divergence between the Atlantic and Mediterranean populations of the common littoral shrimp P. serratus was greater and dated to be much older (4.5-12.3 Ma, Plio-Miocene), so we considered that they could represent two separated species. Therefore, species crypticism in the genus Palaemon seems to be a common phenomenon.
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Affiliation(s)
- Inés González-Castellano
- Departamento de Biología and Centro de Investigaciones Científicas Avanzadas (CICA), Universidade da Coruña, A Coruña, Spain
| | - Joan Pons
- Instituto Mediterráneo de Estudios Avanzados (IMEDEA), Consejo Superior de Investigaciones Científicas (CSIC) and Universitat de les Illes Balears, Esporles, Spain
| | - Enrique González-Ortegón
- Instituto de Ciencias Marinas de Andalucía (ICMAN), Consejo Superior de Investigaciones Científicas (CSIC), Puerto Real, Spain
| | - Andrés Martínez-Lage
- Departamento de Biología and Centro de Investigaciones Científicas Avanzadas (CICA), Universidade da Coruña, A Coruña, Spain
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Zheng C, Ye Z, Zhu X, Zhang H, Dong X, Chen P, Bu W. Integrative taxonomy uncovers hidden species diversity in the rheophilic genus
Potamometra
(Hemiptera: Gerridae). ZOOL SCR 2019. [DOI: 10.1111/zsc.12401] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
- Chenguang Zheng
- Institute of Entomology College of Life Sciences Nankai University Tianjin China
| | - Zhen Ye
- Institute of Entomology College of Life Sciences Nankai University Tianjin China
| | - Xiuxiu Zhu
- Institute of Entomology College of Life Sciences Nankai University Tianjin China
| | | | - Xue Dong
- Institute of Entomology College of Life Sciences Nankai University Tianjin China
| | - Pingping Chen
- Netherlands Biodiversity Centre – Naturalis Leiden The Netherlands
| | - Wenjun Bu
- Institute of Entomology College of Life Sciences Nankai University Tianjin China
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17
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Romanova EV, Bukin YS, Mikhailov KV, Logacheva MD, Aleoshin VV, Sherbakov DY. Hidden cases of tRNA gene duplication and remolding in mitochondrial genomes of amphipods. Mol Phylogenet Evol 2019; 144:106710. [PMID: 31846708 DOI: 10.1016/j.ympev.2019.106710] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2019] [Revised: 12/13/2019] [Accepted: 12/13/2019] [Indexed: 12/30/2022]
Abstract
The evolution of tRNA genes in mitochondrial (mt) genomes is a complex process that includes duplications, degenerations, and transpositions, as well as a specific process of identity change through mutations in the anticodon (tRNA gene remolding or tRNA gene recruitment). Using amphipod-specific tRNA models for annotation, we show that tRNA duplications are more common in the mt genomes of amphipods than what was revealed by previous annotations. Seventeen cases of tRNA gene duplications were detected in the mt genomes of amphipods, and ten of them were tRNA genes that underwent remolding. The additional tRNA gene findings were verified using phylogenetic analysis and genetic distance analysis. The majority of remolded tRNA genes (seven out of ten cases) were found in the mt genomes of endemic amphipod species from Lake Baikal. All additional mt tRNA genes arose independently in the Baikalian amphipods, indicating the unusual plasticity of tRNA gene evolution in these species assemblages. The possible reasons for the unusual abundance of additional tRNA genes in the mt genomes of Baikalian amphipods are discussed. The amphipod-specific tRNA models developed for MiTFi refine existing predictions of tRNA genes in amphipods and reveal additional cases of duplicated tRNA genes overlooked by using less specific Metazoa-wide models. The application of these models for mt tRNA gene prediction will be useful for the correct annotation of mt genomes of amphipods and probably other crustaceans.
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Affiliation(s)
- Elena V Romanova
- Laboratory of Molecular Systematics, Limnological Institute, Irkutsk, Russian Federation.
| | - Yurij S Bukin
- Laboratory of Molecular Systematics, Limnological Institute, Irkutsk, Russian Federation; Faculty of Biology and Soil Studies, Irkutsk State University, Irkutsk, Russian Federation
| | - Kirill V Mikhailov
- Belozersky Institute for Physicochemical Biology, Lomonosov Moscow State University, Moscow, Russian Federation; Institute for Information Transmission Problems of the Russian Academy of Sciences, Moscow, Russian Federation
| | - Maria D Logacheva
- Belozersky Institute for Physicochemical Biology, Lomonosov Moscow State University, Moscow, Russian Federation; Institute for Information Transmission Problems of the Russian Academy of Sciences, Moscow, Russian Federation
| | - Vladimir V Aleoshin
- Belozersky Institute for Physicochemical Biology, Lomonosov Moscow State University, Moscow, Russian Federation; Institute for Information Transmission Problems of the Russian Academy of Sciences, Moscow, Russian Federation
| | - Dmitry Yu Sherbakov
- Laboratory of Molecular Systematics, Limnological Institute, Irkutsk, Russian Federation; Faculty of Biology and Soil Studies, Irkutsk State University, Irkutsk, Russian Federation
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18
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Copilaş-Ciocianu D, Sidorov D, Gontcharov A. Adrift across tectonic plates: molecular phylogenetics supports the ancient Laurasian origin of old limnic crangonyctid amphipods. ORG DIVERS EVOL 2019. [DOI: 10.1007/s13127-019-00401-7] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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